Strange errors?

[Shashank Shastry]

Hi westpa group, 

I have a system running multiple bstates and a single pcoord. I am running into this strange error that i have never seen before. Not entirely sure how to troubleshoot this, any input would be helpful, thanks!

WESTPA environment activating ...
Updating system with the options from the configuration file
Creating HDF5 file '/.../0-Projects/02-systems/04-RTKs/02-fgfr3/03-westpa/01-sym_fgfr3_A391E/west.h5'
1 target state(s) present
Calculating progress coordinate values for basis states.
Traceback (most recent call last):
  File "/.../micromamba/envs/westpa/bin/w_init", line 10, in <module>
    sys.exit(entry_point())
             ^^^^^^^^^^^^^
  File "/.../micromamba/envs/westpa/lib/python3.11/site-packages/westpa/cli/core/w_init.py", line 111, in entry_point
    initialize(
  File "/.../micromamba/envs/westpa/lib/python3.11/site-packages/westpa/cli/core/w_init.py", line 218, in initialize
    sim_manager.initialize_simulation(
  File "/.../micromamba/envs/westpa/lib/python3.11/site-packages/westpa/core/sim_manager.py", line 304, in initialize_simulation
    self.data_manager.create_ibstate_iter_h5file(basis_states)
  File "/.../micromamba/envs/westpa/lib/python3.11/site-packages/westpa/core/data_manager.py", line 562, in create_ibstate_iter_h5file
    self.update_iter_h5file(0, segments)
  File "/.../micromamba/envs/westpa/lib/python3.11/site-packages/westpa/core/data_manager.py", line 577, in update_iter_h5file
    outf.write_segment(segment, True)
  File "/.../micromamba/envs/westpa/lib/python3.11/site-packages/westpa/core/h5io.py", line 698, in write_segment
    self.write(
  File "/.../micromamba/envs/westpa/lib/python3.11/site-packages/mdtraj/formats/hdf5.py", line 911, in write
    self._get_node(where="/", name=name).append(contents)
  File "/.../micromamba/envs/westpa/lib/python3.11/site-packages/tables/earray.py", line 235, in append
    self._check_shape_append(nparr)
  File "/.../micromamba/envs/westpa/lib/python3.11/site-packages/tables/earray.py", line 209, in _check_shape_append
    raise ValueError(
ValueError: the shapes of the appended object and the ``/coordinates`` EArray differ in non-enlargeable dimension 1
srun: error: dgx: task 0: Exited with exit code 1

[Leung, Jeremy]

Hi Shashank,

It's impossible to debug unless we know what exactly you passed to `$WEST_TRAJECTORY_RETURN`. If you load and write with those files as an hdf5 file with mdtraj outside of westpa, do they work? I also know you're dealing with multiple bstates. Start with one first, then add in the rest. `--debug` flag might help, but might swamp you with error message. If that's the case `--verbose` would be good too.

Also judging from the line numbers, you're probably running westpa <= 2022.12 and mdtraj <= 1.11.0. Both of those have been updated in the past month to account for bugs regarding read/write of hdf5 format. It might be worth creating a new environment with westpa v2022.14 and mdtraj 1.11.1 (or `1.11.1.post1` if on pip).

-- JL

---
Jeremy M. G. Leung, PhD
Research Assistant Professor, Chemistry (Chong Lab)
University of Pittsburgh | 219 Parkman Avenue, Pittsburgh, PA 15260
jml...@pitt.edu | [He, Him, His]

On Feb 9, 2026, at 1:01 PM, Shashank Shastry <ss...@illinois.edu> wrote:

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